Fish Taxa

Overview

The taxonomy.fish table provides a standardized reference for all fish taxa observed during Pristine Seas expeditions. It harmonizes scientific names, taxonomic hierarchy, and ecological traits to support robust analysis, reporting, and integration across survey methods.

Each row corresponds to a unique accepted AphiaID from the World Register of Marine Species (WoRMS), and includes the scientific name, taxonomic ranks, common names, trophic group, length–weight parameters, and habitat classification.

This table supports three core functions:

• Taxonomic resolution — reconciles field-recorded names with accepted nomenclature
• Trait-based analysis — enables grouping by trophic guild, habitat, and life history traits
• Cross-dataset integration — provides a consistent key (accepted_aphia_id) to link observations, field codes, and traits

Taxa originate from underwater visual surveys (UVS), BRUV deployments, and regional species checklists compiled from both internal and external sources.

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Data Sources

The table integrates multiple curated sources to ensure taxonomic consistency and trait completeness:

• Pristine Seas Field Records
  Derived from diver-entered codes, fieldbooks, and expedition species lists across UVS, BRUVS, and other survey methods. These are reconciled with accepted WoRMS entries.

• Akiona et al.
  A curated dataset of Pacific reef fishes, their length–weight parameters, and trophic classification, developed by researchers at Scripps Institution of Oceanography. This dataset provides key life history traits (e.g., maximum length, a and b coefficients) and has been manually corrected and standardized for integration.

• World Register of Marine Species (WoRMS)
  Used as the taxonomic backbone. Each taxon is linked to an accepted AphiaID, with full lineage (kingdom to species) and synonym resolution.

• FishBase (via rfishbase)
  Supplements trait fields such as trophic level, common names, and ecological notes, and fills gaps not covered by Akiona.

Together, these sources provide a robust, reproducible foundation for trait-based ecological analysis.

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Structure

Taxonomy

These fields define the accepted scientific identity and taxonomic lineage of each record (Table 1). Only valid names are stored here; upstream synonym handling is managed through the uvs_fish_codes table.

All taxa are matched to an accepted AphiaID from WoRMS, ensuring global consistency and traceability. These fields enable spatial and ecological grouping, support taxonomic joins, and serve as the foundation for trait integration.

Table 1: Taxonomic lineage fields for fish taxa in the Pristine Seas Database.

Field	Type	Required	Description
accepted_name	STRING	true	Valid scientific name (Genus species), standardized using WoRMS.
accepted_aphia_id	INTEGER	true	Unique WoRMS identifier for the accepted name.
rank	STRING	true	Taxonomic rank of the record (species, genus, or family).
genus	STRING	false	Genus of the accepted name.
family	STRING	false	Family of the accepted name.
order	STRING	false	Order of the accepted name.
class	STRING	true	Class of the accepted name.
phylum	STRING	true	Phylum of the accepted name.
kingdom	STRING	true	Kingdom of the accepted name.

Common Names

Each record includes species and family level common names to support communication, outreach, and summary reporting. Names are sourced from FishBase and manually curated regional records

Table 2: Common names fields for fish taxa in the Pristine Seas Database.

Field	Type	Required	Description
common_name	STRING	false	Primary English common name, sourced from FishBase or regional sources.
common_family	STRING	false	Generalized family name used for communication and summaries (e.g., wrasses, groupers).

Trophic Traits

Trophic traits classify each fish taxon based on diet and ecological role in the food web. These fields support functional grouping, biomass estimation, and ecosystem-based analysis.

The trophic_group field is the most important and is used extensively in Pristine Seas reporting. It is primarily sourced from Akiona et al., with manual curation and expert input for non-Pacific species. Other fields are derived from FishBase via rfishbase.

Broad Trophic Groups

• herbivore/detritivore
  
• planktivore
  
• lower-carnivore
  
• top-predator
  
• shark
  
• unknown

Table 3: Schema for trophic traits in taxonomy.fish.

Field	Type	Required	Description
trophic_group	STRING	false	Expert-assigned ecological role from Akiona et al. or internal classification. One of: ‘herbivore/detritivore’, ‘planktivore’, ‘lower-carnivore’, ‘top-predator’, ‘shark’, ‘unknown’.
trophic_lvl	FLOAT	false	Numeric trophic level estimate from FishBase.
trophic_lvl_se	FLOAT	false	Standard error of the trophic level estimate (FishBase).
feeding_path	STRING	false	Primary foraging environment, e.g., ‘benthic’, ‘pelagic’, ‘non-feeding’ (FishBase).
feeding_type	STRING	false	Behavioral feeding mode such as ‘ambush predator’, ‘filter feeder’ (FishBase).
diet	STRING	false	General dietary category from FishBase.

Morphometrics

Morphometric traits capture species-level body size and length–weight relationships. These are critical for estimating fish biomass from underwater visual survey data and for modeling size-based ecological dynamics.

This section integrates manually curated values from Akiona et al. with supplemental data from FishBase. Preference is given to Akiona parameters when available, as they are regionally validated and quality-checked. FishBase entries are used to fill remaining gaps.

The table includes:

• Maximum total length (tl_max): typically sourced from FishBase, but may also reflect expert field observations or literature.
• Length–weight relationship parameters (lw_a, lw_b): coefficients from the equation W = a × Lᵇ.
• Length type (lw_type) and conversion ratio (ltl_ratio): indicate whether parameters are based on TL, SL, or FL and how to convert them.
• Source fields for all traits to enable auditing and transparency.

Table 4: Schema for morphometric traits in taxonomy.fish.

Field	Type	Required	Description
tl_max	FLOAT	false	Maximum total length (TL) in cm from FishBase, Akiona, or field observation.
tl_max_source	STRING	false	Source of max length (FishBase, SIO, field, or literature).
lw_a	FLOAT	false	Length–weight coefficient ‘a’ in W = a × Lᵇ. Used to estimate biomass.
lw_b	FLOAT	false	Length–weight exponent ‘b’ in W = a × Lᵇ.
ltl_ratio	FLOAT	false	Length-to-length conversion ratio (e.g., SL to TL) when parameters are based on non-TL metrics.
lw_type	STRING	false	Type of length used in the LW relationship (TL, SL, FL, etc.).
lw_source	STRING	false	Provenance of the LW parameters (e.g., Akiona, FishBase, or literature).

Habitat

The habitat_zone field classifies each species into a broad ecological zone based on FishBase and internal harmonization. This trait is useful for filtering species by habitat and summarizing community structure across environments.

• habitat_zone
  Broad habitat category based on FishBase definitions. One of:

  • reef-associated
    
  • benthopelagic
    
  • demersal
    
  • pelagic
    
  • pelagic-neritic
    
  • pelagic-oceanic
    
  • bathypelagic
    
  • bathydemersal
    
  • unknown

Fishery importance

The fishery_importance field classifies each species based on its significance to commercial and subsistence fisheries. This trait supports conservation planning, fisheries impact assessments, and the identification of species with cultural or economic relevance.

Values are sourced primarily from the Importance field in FishBase and are supplemented with expert knowledge and local observations from Pristine Seas expeditions where needed.

• fishery_importance
  Significance to commercial and subsistence fisheries based on FishBase definitions:

  • highly commercial
    
  • commercial
    
  • minor commercial
    
  • subsistence fisheries
    
  • of no interest
    
  • of potential interest

Conservation Status (IUCN)

The taxonomy.fish table includes fields derived from the IUCN Red List to support biodiversity assessments and conservation planning. Each species is matched to its most recent listing (SIS ID) and assigned a standardized category (e.g., LC, NT, VU, EN, CR).

Summary

Overall, the taxonomy.fish table contains 2085 entries, representing 2020 unique taxa across 120 families (Figure 2). The majority of records are teleost fishes, with 1973 taxa, while elasmobranchs account for 47 taxa.

Figure 1: Missingness in the fish taxonomy table

Our database has excellent coverage for all core identity fields, including taxonomy and length-weight parameters. However, we still have work to do to fill gaps in trophic traits, habitat associations, and fisheries importance (Figure 1)

Taxa by Family

Figure 2: Number of species by order and family

The best represented families include (Figure 3):

• Wrasses (families: Labridae and Scaridae) with 182 and 52 species, respectively.
• Gobies (families Gobidae and Microdesmidae) with 199 and 26 species, respectively.
• Damselfishes (family: Pomacentridae) with 182 species
• Cardinalfishes (family: Apogonidae) with 100 species.

Taxa by Trophic Group

Most species in the dataset are classified as Lower-carnivores, with 754 species, followed by 281 planktivores and 205 herbivores/detritivores. The dataset also includes 100 top predators—such as groupers, snappers, and jacks—and 14 sharks.

Figure 3: Number of species by common family and trophic group

Most species in the dataset are classified as reef-associated with a primarily benthic feeding pathway (Figure 4).

Figure 4: Number of species by habitat zone and feeding path

Additionally, according to FishBase, the majority of species have some level of importance to fisheries, whether for subsistence or commercial purposes (Figure 5).

Figure 5: Number of species by family and human use